// -*- c++ -*-
/*****************************************************************************/
// Copyright (c) Illumina 2008
// Author: Richard Shaw
//
// This software is covered by the "Illumina Genome Analyzer Software
// License Agreement" and the "Illumina Source Code License Agreement",
// and certain third party copyright/licenses, and any user of this
// source file is bound by the terms therein (see accompanying files
// Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
// Illumina_Source_Code_License_Agreement.pdf and third party
// copyright/license notices).
/*****************************************************************************/

#ifndef QUALITY_VALUE_STATS_SET_H
#define QUALITY_VALUE_STATS_SET_H

/*****************************************************************************/

#include <stdint.h>

#include <iostream>
#include <map>

#include <stdint.h>

#include "statistics/Read_Align_Info.h"

/*****************************************************************************/

class Quality_Value_Stats_Set
{
    friend std::ostream& operator<<(std::ostream&,
                                    const Quality_Value_Stats_Set&);

 public:
    Quality_Value_Stats_Set();
    ~Quality_Value_Stats_Set();

    void add_read_align_info(const Read_Align_Info& read_align_info);

 private:
    typedef std::map<int, uint64_t> Qual_Val_Freq_Map;
    typedef Qual_Val_Freq_Map::const_iterator Qual_Val_Freq_Map_CIter;
    typedef Qual_Val_Freq_Map::const_reverse_iterator Qual_Val_Freq_Map_CRIter;

    Qual_Val_Freq_Map my_qual_val_freq_map;
    Qual_Val_Freq_Map my_errs_by_qual_val_freq_map;
    uint64_t my_num_bases;
};

/*****************************************************************************/

std::ostream& operator<<(std::ostream& ostrm,
                         const Quality_Value_Stats_Set&
                         quality_value_stats_set);

/*****************************************************************************/

#endif // ! QUALITY_VALUE_STATS_SET_H

/*****************************************************************************/